Modeling from reference; how to not get messed up?
You can select only the geometry you want to edit and press ShiftH to Hide everything else but the selection.

From the Top View this looks unmanageable:



So we go to Side View, select only the vertices we need, and hide everything else. (ShiftH)



Of course the top view also shows just the vertices that we have left visible. Much easier to manage:



You can then reveal the hidden geometry again when you're done editing by pressing AltH

Extra tips

Although pressing ShiftH will hide everything but your selection, pressing just H will hide the selection and leave everything else as-is. Un-hiding is the same (AltH) no matter which Hide method you have used.

This also works in Object Mode. You can hide and reveal objects in the same way.